PyRenew: A Package for Bayesian Renewal Modeling with JAX and NumPyro.

⚠️ This is a work in progress ⚠️

pyrenew is a flexible tool for simulation and statistical inference of epidemiological models, emphasizing renewal models. Built on top of the numpyro Python library, pyrenew provides core components for model building, including pre-defined models for processing various types of observational processes. To start, visit the tutorials section on the project's website here.

The following diagram illustrates the composition of the HospitalAdmissionsModel class. Notably, all components are modular and can be replaced with custom implementations.

flowchart LR

  %% Elements
  rt_proc["Random Walk Rt\nProcess (latent)"];
  latent_inf["Latent Infections"]
  latent_ihr["Infection to Hosp.\nrate (latent)"]
  neg_binom["Observation process\n(hospitalizations)"]
  latent_hosp["Latent Hospitalizations"];
  i0["Initial infections\n(latent)"];
  gen_int["Generation\ninterval (fixed)"];
  hosp_int["Hospitalization\ninterval (fixed)"];

  %% Models
  basic_model(("Infections\nModel"));
  admin_model(("Hospital Admissions\nModel"));

  %% Latent infections
  rt_proc --> latent_inf;
  i0 --> latent_inf;
  gen_int --> latent_inf;
  latent_inf --> basic_model

  %% Hospitalizations
  hosp_int --> latent_hosp

  neg_binom --> admin_model;
  latent_ihr --> latent_hosp;
  basic_model --> admin_model;
  latent_hosp --> admin_model;

Installation

Install via pip with

pip install git+https://github.com/CDCgov/PyRenew@main

Models Implemented With PyRenew

CDCgov/pyrenew-covid-wastewater: Models and infrastructure for forecasting COVID-19 hospitalizations using wastewater data with PyRenew.
CDCgov/pyrenew-flu-light: An instantiation in PyRenew of an influenza forecasting model used in the 2023-24 respiratory season.

Resources

The MSR Website provides general documentation and tutorials on using MSR.
The Model Equations Sheet describe the mathematics of the renewal processes and models MSR supports.
Additional reading on renewal processes in epidemiology
- Semi-mechanistic Bayesian modelling of COVID-19 with renewal processes
- Unifying incidence and prevalence under a time-varying general branching process

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CDCgov / PyRenew

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